De novo proteins from random sequences through in vitro evolution

Tong, Cher Ling; Lee, Kun Hwa; Seelig, Burckhard

doi:10.1016/j.sbi.2020.12.014

Cited by 8 publications

(5 citation statements)

References 47 publications

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“…The properties of the random sequence libraries presented in this study have direct implications for the evolution of proteins in extant biology, as well as in the earlies pre-LUCA period. However, the results presented here as well as the suggested follow-up studies are also of prime relevance to comprehending dark protein space and to evolving novel strategies of protein design principles [61–63].…”

Section: Discussionmentioning

confidence: 99%

Modern and prebiotic amino acids support distinct structural profiles in proteins

et al. 2022

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The earliest proteins had to rely on amino acids available on early Earth before the biosynthetic pathways for more complex amino acids evolved. In extant proteins, a significant fraction of the ‘late’ amino acids (such as Arg, Lys, His, Cys, Trp and Tyr) belong to essential catalytic and structure-stabilizing residues. How (or if) early proteins could sustain an early biosphere has been a major puzzle. Here, we analysed two combinatorial protein libraries representing proxies of the available sequence space at two different evolutionary stages. The first is composed of the entire alphabet of 20 amino acids while the second one consists of only 10 residues (ASDGLIPTEV) representing a consensus view of plausibly available amino acids through prebiotic chemistry. We show that compact conformations resistant to proteolysis are surprisingly similarly abundant in both libraries. In addition, the early alphabet proteins are inherently more soluble and refoldable, independent of the general Hsp70 chaperone activity. By contrast, chaperones significantly increase the otherwise poor solubility of the modern alphabet proteins suggesting their coevolution with the amino acid repertoire. Our work indicates that while both early and modern amino acids are predisposed to supporting protein structure, they do so with different biophysical properties and via different mechanisms.

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Section: Discussionmentioning

confidence: 99%

Modern and prebiotic amino acids support distinct structural profiles in proteins

et al. 2022

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“…Furthermore, we were recently able to demonstrate that while structured random proteins are hard to express in vivo due to their higher aggregation propensity, random proteins with greater ID are readily tolerated by Escherichia coli 26 . Simultaneously, at least some protein folds appear to be relatively evolvable from random sequences 28 . For example, Hayashi et al 29 were able to evolve an arbitrary random sequence to replace the D2 domain of an essential bacteriophage protein.…”

Section: Mainmentioning

confidence: 99%

Experimental characterization of de novo proteins and their unevolved random-sequence counterparts

et al. 2023

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De novo gene emergence provides a route for new proteins to be formed from previously non-coding DNA. Proteins born in this way are considered random sequences and typically assumed to lack defined structure. While it remains unclear how likely a de novo protein is to assume a soluble and stable tertiary structure, intersecting evidence from random sequence and de novo-designed proteins suggests that native-like biophysical properties are abundant in sequence space. Taking putative de novo proteins identified in human and fly, we experimentally characterize a library of these sequences to assess their solubility and structure propensity. We compare this library to a set of synthetic random proteins with no evolutionary history. Bioinformatic prediction suggests that de novo proteins may have remarkably similar distributions of biophysical properties to unevolved random sequences of a given length and amino acid composition. However, upon expression in vitro, de novo proteins exhibit moderately higher solubility which is further induced by the DnaK chaperone system. We suggest that while synthetic random sequences are a useful proxy for de novo proteins in terms of structure propensity, de novo proteins may be better integrated in the cellular system than random expectation, given their higher solubility.

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“…Using modern tools of synthetic biology, several groups have mimicked random sequences from the canonical alphabet or its reduced subsets, in search of their general properties (summarized in Tong et al . [139]). In short, random sequences can inherently form secondary structures similar to their occurrence in biological proteins and between 5 and 20% of random peptides of lengths 80–100 amino acids have been reported capable of undergoing compaction/folding [140–143].…”

Section: Amino Acid Alphabetsmentioning

confidence: 99%

Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids

Fried

Fujishima

Makarov

et al. 2022

J. R. Soc. Interface.

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Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative ‘peptide-polynucleotide stage’. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.

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De novo proteins from random sequences through in vitro evolution

Cited by 8 publications

References 47 publications

Modern and prebiotic amino acids support distinct structural profiles in proteins

Modern and prebiotic amino acids support distinct structural profiles in proteins

Experimental characterization of de novo proteins and their unevolved random-sequence counterparts

Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids

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